Thanks for your reply Justin... But these pressure I provided here are by doing the gmx energy -f energy.edr And then selecting the pressure from the list. It only shows these values for respective temperature windows after 1st stage of equillibration.. What should I do? How do I know what is the actual pressure of my system? Or is there any pressure convergence protocol in REMD? Thanks in advance -Soham
On Sat, 19 May 2018, 9:11 pm Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 5/19/18 8:45 AM, Soham Sarkar wrote: > > Thanks for reply.. but what is the actual pressure of the system? You > > mentioned it as the instantaneous pressure > > Instantaneous simply refers to the value at any given time point; these > will fluctuate wildly, particularly for a tiny system like yours, and > the instantaneous values are meaningless. > > The average pressure (and its distribution) is more meaningful. Compute > that with gmx energy. > > -Justin > > > On Sat, 19 May 2018, 6:03 pm Mark Abraham, <mark.j.abra...@gmail.com> > wrote: > > > >> Hi, > >> > >> This is normal for instantaneous measurements of pressure. See > >> http://www.gromacs.org/Documentation/Terminology/Pressure > >> > >> Mark > >> > >> On Sat, May 19, 2018, 13:04 Soham Sarkar <soham9...@gmail.com> wrote: > >> > >>> Dear All, > >>> I have a small system including a 4 residue peptide. I have chosen 8 > >>> temperature windows for doing REMD simulation of this system. After the > >>> temperature convergence of the 8 systems in the 1st stage of > >> equillibration > >>> run, the obtained pressure are quite absurd, which is not change that > >> much > >>> after the 2nd stage of production run. I want to know whether this type > >> of > >>> pressure range is ok for a system or not? Should I carry out analysis > in > >>> this pressure range? As in normal md simulation there is a pressure > >>> convergence step which takes the system to the desired pressure. This > >> type > >>> of step is not there in the REMD simulation. > >>> The pressure and temperature of this system after 1st stage of > >>> equillibration of 10ns are as follows > >>> Temperature(K) Pressure(Bar) > >>> 350.112 -28.4761 > >>> 369.218 262.054 > >>> 389.201 592.84 > >>> 410.074 946.021 > >>> 429.12 1273.92 > >>> 448.873 1628.61 > >>> 469.438 2005.04 > >>> 490.272 2392.50 > >>> > >>> > >>> -- > >>> SOHAM SARKAR > >>> Junior Research Fellow > >>> Department of Chemistry > >>> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.